[gmx-users] ions problem

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 16 20:37:09 CEST 2011

ahmet yıldırım wrote:
> Dear users,
> I am using gromacs 4.5.3. Initially I removed ligands from pdb file. 
> Then I started to simulation .I met such a problem ( last error) after I 
> added ions. What could be the problem?
> pdb2gmx -f withoutligand_xxx.pdb
> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> *Fatal Error:*
> System has non-zero total charge: -1.500000e+01
> genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log

Unless you updated your topology manually after running this command, you 
haven't accounted for the fact that 15 water molecules are going to be removed. 
  Use the -p flag to have genion make the changes for you.  Note that "NA+" is 
incorrect for version 4.5.3 - ion [moleculetype] names have changed since 
version 4.0.7.

> select: Group 13 (SOL)
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> *Fatal error:*
> number of coordinates in coordinate file (solvated.gro, 106473)
> does not match topology (topol.top, 106518)

The answer to this error is _always_ the same - you haven't accounted properly 
for some change in the system that has been made to the coordinate file but not 
the topology.


> _*topol.top:*_
> ..
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> SOL                   185
> SOL                   143
> SOL                33723
> NA                       15

Something isn't matching up here.  Either your genion command that you showed 
above is wrong, or this topology snippet has been modified from what genion 
would produce.  Please always copy and paste commands, topology snippets, etc so 
that we have self-consistent information to help you.


> -- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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